Publikationen von Berend L. de Groot
Alle Typen
Zeitschriftenartikel (212)
1.
Zeitschriftenartikel
Quantification of the Impact of Structure Quality on Predicted Binding Free Energy Accuracy. Journal of Chemical Information and Modeling (2025)
2.
Zeitschriftenartikel
122 (21), e2423866122 (2025)
Effective polarization in potassium channel simulations: Ion conductance, occupancy, voltage response, and selectivity. Proceedings of the National Academy of Sciences of the United States of America 3.
Zeitschriftenartikel
16, S. 9357 - 9365 (2025)
Identification of allosteric sites and ligand-induced modulation in the dopamine receptor through large-scale alchemical mutation scan. Chemical Science 4.
Zeitschriftenartikel
21 (8), S. 4095 - 4106 (2025)
Improving pKa Predictions with Reparameterized Force Fields and Free Energy Calculations. Journal of Chemical Theory and Computation 5.
Zeitschriftenartikel
22, S. 641 - 645 (2025)
The need to implement FAIR principles in biomolecular simulations. Nature Methods 6.
Zeitschriftenartikel
129 (11), S. 2882 - 2902 (2025)
Prospective Evaluation of Structure-Based Simulations Reveal Their Ability to Predict the Impact of Kinase Mutations on Inhibitor Binding. The Journal of Physical Chemistry B 7.
Zeitschriftenartikel
46 (5), e70059 (2025)
Scaling of the GROMACS Molecular Dynamics Code to 65k CPU Cores on an HPC Cluster. Journal of Computational Chemistry 8.
Zeitschriftenartikel
28, S. 259 - 267 (2025)
NOMPC ion channel hinge forms a gating spring that initiates mechanosensation. Nature Neuroscience 9.
Zeitschriftenartikel
16, 760 (2025)
Lipidic folding pathway of α-Synuclein via a toxic oligomer. Nature Communications 10.
Zeitschriftenartikel
88, 102887 (2024)
Biomolecular simulations at the exascale: From drug design to organelles and beyond. Current Opinion in Structural Biology 11.
Zeitschriftenartikel
123 (19), S. 3408 - 3420 (2024)
Effect of two activators on the gating of a K2P channel. Biophysical Journal 12.
Zeitschriftenartikel
12, RP90851 (2024)
Structure and dynamics of cholesterol-mediated aquaporin-0 arrays and implications for lipid rafts. eLife 13.
Zeitschriftenartikel
3 (7), pgae272 (2024)
Selectivity filter mutations shift ion permeation mechanism in potassium channels. PNAS Nexus 14.
Zeitschriftenartikel
45 (17), S. 1444 - 1455 (2024)
Resolving coupled pH titrations using alchemical free energy calculations. Journal of Computational Chemistry 15.
Zeitschriftenartikel
64 (13), S. 5063 - 5076 (2024)
Current State of Open Source Force Fields in Protein–Ligand Binding Affinity Predictions. Journal of Chemical Information and Modeling 16.
Zeitschriftenartikel
121 (7), e2319682121 (2024)
Molecular basis for human aquaporin inhibition. PNAS 17.
Zeitschriftenartikel
20 (2), S. 914 - 925 (2024)
Guidelines for Free-Energy Calculations Involving Charge Changes. Journal of Chemical Theory and Computation 18.
Zeitschriftenartikel
19 (21), S. 7833 - 7845 (2023)
Accurately Predicting Protein pKa Values Using Nonequilibrium Alchemy. Journal of Chemical Theory and Computation 19.
Zeitschriftenartikel
155 (8), e202213166 (2023)
Interactions between selectivity filter and pore helix control filter gating in the MthK channel. Journal of General Physiology 20.
Zeitschriftenartikel
19 (9), S. 2574 - 2589 (2023)
Ion Conduction Mechanisms in Potassium Channels Revealed by Permeation Cycles. Journal of Chemical Theory and Computation